INDEX

1. Setting the working directory (wd)
2. Loading packages
3. Building the data table
4. Saving background image & Plotting

PACKAGES

• install.packages(“png”)
• install.packages(“imager”)
• install.packages(“magrittr”)
• install.packages(“ggimage”)
• install.packages(“ggpubr”)
• devtools::install_github(“brendan-R/brocks”)

1. Loading packages

library("magrittr")
library("png")
library("imager")
library("dplyr")
library("tidyr")
library("ggplot2")
library("jpeg")
library("grid")
library("plotly")
library("brocks")
library("ggpubr")

2. Setting the working directory

setwd("/Users/davidizquierdogomez/Desktop/schemalegende")

3. Building the grid

grid <- as_tibble(rep(seq(0, 10, by = 0.5), 21)) %>%
         arrange(value) %>% 
         cbind(rep(seq(0, 10, by = 0.5), 21), rep(0, 441)) %>% 
         rename(x = "value") %>%
         rename(y = "rep(seq(0, 10, by = 0.5), 21)") %>% 
         rename(n = "rep(0, 441)") %>%
         mutate(n = as.character(n)) %>% 
         # mutate(x = as.character(x), y = as.character(y)) %>%
         # mutate(n = as.character(n)) %>% 
         arrange(x, y)

4. Plotly grid to identify landmarks

image_destination <- "https://raw.githubusercontent.com/davidizquierdogomez/pictures/main/hellocellschema.png"

ggrid <- ggplot(data = grid, aes(x = x, y = y)) +
  geom_point(size = 1, colour = "red") +
  scale_y_continuous(expand = c(0,0), limits = c(0, max(grid$y))) +
  scale_x_continuous(expand = c(0,0), limits = c(0, max(grid$x))) +
  # geom_text(aes(label = n), vjust = 1.5, colour = "black") +
  theme_bw() +
  theme(plot.title = element_text(size = rel(1.5), face = "bold", vjust = 1.5),
        axis.line = element_blank(),
        axis.text.x = element_blank(),
        axis.text.y = element_blank(),
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        axis.ticks.x = element_blank(),
        axis.ticks.y = element_blank(),
        panel.border = element_blank(),
        panel.background = element_blank(),
        plot.margin = unit(c(4,0,0,4), "cm")) + #plot margins margin(t,r,b,l)
  ggtitle("Cellule eucaryote") +
  theme(plot.title = element_text(size = 15, hjust = 0.5, colour = "red")) +
  labs(x="David Izquierdo")

ppgrid <- ggplotly(ggrid, width = 800, height = 600) %>% 
   config(displayModeBar = F)
ttgrid <- plotly::layout(ppgrid,
               autosize = TRUE,
               xaxis = list(showgrid = F),
               yaxis = list(showgrid = F),
  images = list(
  list(
    source =  image_destination,
    xref = "x",
    yref = "y",
    x = 0,
    y = 10,
    sizex = 10,
    sizey = 10,
    sizing = "stretch",
    opacity = 0.9,
    layer = "below"
  )
))

ttgrid

Final Interactive figure

# FINAL COORDINATES
# create the vectors

xfinal <- c(4.50, 1.50, 3.00, 7.00, 1.00, 7.00, 6.50, 5.00, 4.00, 6.00, 5.00, 9.50, 9.50, 5.00, 1.50, 4.50, 5.40, 5.00)
yfinal <- c(8.00, 6.00, 4.00, 6.50, 4.50, 4.50, 8.00, 3.00, 5.50, 6.50, 1.00, 7.50, 5.50, 9.50, 5.00, 3.50, 9.00, 8.50)
labelfinal <- c("Nucléole",
                "Centrosome",
                "Mitochondrie",
                "Mitochondrie",
                "Cytosquelette",
                "Golgi",
                "Lysosome",
                "Lysosome",
                "Ret.End.Rugueux",
                "Ret.End.Lisse",
                "Membrane Plasmique",
                "Cils",
                "Cils",
                "Enveloppe nucléaire",
                "Ribosome",
                "Cytoplasme",
                "Pore nucléaire",
                "Chromatine")

# bind the vectors into a tibble

coo_cellule <- cbind(xfinal, yfinal) %>%
   as_tibble(xfinal, yfinal) %>%
   mutate(label = labelfinal) %>% 
   rename(x = xfinal, y = yfinal) %>% 
   arrange(x, y)


gg <- ggplot(data = coo_cellule, aes(x = x, y = y, text = label)) +
  geom_point(size = 2, pch = 21, bg="black", lwd=2, colour = "yellow") +
  scale_y_continuous(expand = c(0,0), limits = c(0, max(grid$y))) +
  scale_x_continuous(expand = c(0,0), limits = c(0, max(grid$x))) +
  theme_bw() +
  theme(plot.title = element_text(size = rel(1.5), face = "bold", vjust = 1.5),
        axis.line = element_blank(),
        axis.text.x = element_blank(),
        axis.text.y = element_blank(),
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        axis.ticks.x = element_blank(),
        axis.ticks.y = element_blank(),
        panel.border = element_blank(),
        panel.background = element_blank(),
        # panel.border = element_rect(colour = "white", fill=NA, size=1),
        plot.margin = unit(c(4,0,0,4), "cm")) + #plot margins margin(t,r,b,l)
  ggtitle("Cellule eucaryote") +
  theme(plot.title = element_text(size = 25, hjust = 0.5, colour = "red")) +
  labs(x="David Izquierdo")

## Warning: Duplicated aesthetics after name standardisation: size

pp <- ggplotly(gg, width = 800, height = 600, tooltip = "label") %>% 
   config(displayModeBar = F)
tt <- plotly::layout(pp,
               autosize = TRUE,
               xaxis = list(showgrid = F),
               yaxis = list(showgrid = F),
  images = list(
  list(
    source =  image_destination,
    xref = "x",
    yref = "y",
    x = 0,
    y = 10,
    sizex = 10,
    sizey = 10,
    sizing = "stretch",
    opacity = 0.9,
    layer = "below"
  )
))

tt

CORRECTION

# the image must be fetched locally

img <- readPNG("/Users/davidizquierdogomez/Desktop/schemalegende/hellocellschema.png")

plotcorrection <- ggplot(coo_cellule,aes(x=x,y=y)) + 
  annotation_custom(rasterGrob(img, width = unit(1,"npc"), height = unit(1,"npc")), 
                    -Inf, Inf, -Inf, Inf) +
  scale_y_continuous(expand = c(0,0), limits = c(0, 10)) +
  scale_x_continuous(expand = c(0,0), limits = c(0, 10)) +
  geom_point(size = 2, pch = 21, bg="black", colour = "yellow") +
  ggrepel::geom_label_repel(aes(label = label), size = 5) +
  theme_bw() +
  theme(plot.title = element_text(size = rel(1.5), face = "bold", vjust = 1.5),
        axis.line = element_blank(),
        axis.text.x = element_blank(),
        axis.text.y = element_blank(),
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        axis.ticks.x = element_blank(),
        axis.ticks.y = element_blank(),
        panel.border = element_rect(colour = "white", fill = NA, size = 1),
        panel.background = element_blank()) +
  ggtitle("\nCellule eucaryote\n\n") +
  theme(plot.title = element_text(size = 20, hjust = 0.5, colour = "red")) +
  labs(x="David Izquierdo")

plotcorrection